Mercurial > repos > iuc > micro_decon
diff micro_decon.xml @ 0:bd267e082f86 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon/ commit bb37578aa61bf4a47af262e02baf0a1c1d9d02c6
| author | iuc |
|---|---|
| date | Wed, 06 Aug 2025 08:38:24 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/micro_decon.xml Wed Aug 06 08:38:24 2025 +0000 @@ -0,0 +1,164 @@ +<tool name="micro_decon" id="micro_decon" version="@TOOL_VERSION@+@VERSION_SUFFIX@" profile="24.2" license="@LICENSE@"> + <description>removing contamination from metabarcoding</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="creators"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/decon.R' + --mode $function_cond.function_selector + --data_file '$input_table' + #set mode = $function_cond.function_selector + #if $mode != 'remove_thresh': + --numb_blanks '$function_cond.numb_blanks' + #end if + + #if $mode != 'remove_cont' + --numb_ind 'c($function_cond.numb_ind)' + #end if + + #if $mode in ['decon', 'remove_cont']: + --runs '$function_cond.runs' + --regression '$function_cond.regression' + --low_threshold '$function_cond.low_threshold' + --up_threshold '$function_cond.up_threshold' + #end if + + #if $mode in ['decon', 'remove_thresh']: + --thresh '$function_cond.thresh' + --prop_thresh '$function_cond.prop_thresh' + #end if + + #if $mode == 'decon_diff': + --output '$function_cond.output' + #end if + --taxa '$taxa' + ]]></command> + <inputs> + <param name="input_table" type="data" format="csv,tsv,tabular" label="Input table"/> + <param argument="--taxa" type="boolean" label="Does the input table contains taxonomy column?" value="true" truevalue="T" falsevalue="F"/> + <conditional name="function_cond"> + <param name="function_selector" type="select" label="Select the microDecon function to apply"> + <option value="decon">decon</option> + <option value="remove_cont">remove.cont</option> + <option value="remove_thresh">remove.thresh</option> + <option value="decon_diff">decon.diff</option> + </param> + <when value="decon"> + <expand macro="numb_blanks_arg"/> + <expand macro="numb_ind_arg"/> + <expand macro="runs_and_regression_args"/> + <expand macro="thresh_args"/> + </when> + <when value="remove_cont"> + <expand macro="numb_blanks_arg"/> + <expand macro="runs_and_regression_args"/> + </when> + <when value="remove_thresh"> + <expand macro="numb_ind_arg"/> + <expand macro="thresh_args"/> + </when> + <when value="decon_diff"> + <param argument="--output" type="data" label="The output table of remove.cont or remove.thresh" format="csv"/> + <expand macro="numb_blanks_arg"/> + <expand macro="numb_ind_arg"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="decon_table" format="csv" label="${function_cond.function_selector} on ${on_string}: Decontaminated table" from_work_dir="decon_table.csv"/> + <data name="reads_removed" format="csv" label="${function_cond.function_selector} on ${on_string}: Reads removed" from_work_dir="reads_removed.csv"> + <filter>function_cond['function_selector'] != "remove_cont" and function_cond['function_selector'] != "remove_thresh"</filter> + </data> + <data name="difference_sum" format="csv" label="${function_cond.function_selector} on ${on_string}: Difference sum" from_work_dir="difference_sum.csv"> + <filter>function_cond['function_selector'] != "remove_cont" and function_cond['function_selector'] != "remove_thresh"</filter> + </data> + <data name="difference_mean" format="csv" label="${function_cond.function_selector} on ${on_string}: Difference mean" from_work_dir="difference_mean.csv"> + <filter>function_cond['function_selector'] != "remove_cont" and function_cond['function_selector'] != "remove_thresh"</filter> + </data> + <data name="otus_removed" format="csv" label="${function_cond.function_selector} on ${on_string}: OTUs removed" from_work_dir="OTUs_removed.csv"> + <filter>function_cond['function_selector'] != "remove_cont" and function_cond['function_selector'] != "remove_thresh"</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="5"> + <param name="input_table" value="input.csv"/> + <param name="taxa" value="true"/> + <conditional name="function_cond"> + <param name="function_selector" value="decon"/> + <param name="numb_ind" value="3,2"/> + </conditional> + <output name="decon_table" file="decon_table.csv"/> + <output name="reads_removed" file="reads_removed.csv"/> + <output name="difference_sum" file="difference_sum.csv"/> + <output name="difference_mean" file="difference_mean.csv"/> + <output name="otus_removed" file="otus_removed.csv"/> + </test> + <test expect_num_outputs="1"> + <param name="input_table" value="input.csv"/> + <param name="taxa" value="true"/> + <conditional name="function_cond"> + <param name="function_selector" value="remove_cont"/> + </conditional> + <output name="decon_table" file="remove_cont_decon_table.csv"/> + </test> + <test expect_num_outputs="1"> + <param name="input_table" value="remove_cont_decon_table.csv"/> + <param name="taxa" value="true"/> + <conditional name="function_cond"> + <param name="function_selector" value="remove_thresh"/> + <param name="numb_ind" value="3,2"/> + </conditional> + <output name="decon_table" file="remove_thresh_decon_table.csv"/> + </test> + <test expect_num_outputs="5"> + <param name="input_table" value="input.csv"/> + <param name="taxa" value="true"/> + <conditional name="function_cond"> + <param name="function_selector" value="decon_diff"/> + <param name="numb_ind" value="3,2"/> + <param name="output" value="remove_thresh_decon_table.csv"/> + </conditional> + <output name="decon_table" file="decon_table.csv"/> + <output name="reads_removed" file="reads_removed.csv"/> + <output name="difference_sum" file="difference_sum.csv"/> + <output name="difference_mean" file="difference_mean.csv"/> + <output name="otus_removed" file="otus_removed.csv"/> + </test> + </tests> + <help><![CDATA[ +microDecon +========== +The microDecon package is designed to remove contaminant reads from +metabarcoding studies (e.g., from bacterial contamination in reagents during a microbiome +study). + +Input +------ +A table of metabarcoding data structured as a data +frame where each row is an OTU (or ASV or other metabarcoding output), each column is an +individual sample, and each cell contains the number of reads for a given OTU for a given +individual. Additionally, the first column should contain OTU IDs (these can be numeric or +characters), and the last column should (optionally) contain taxonomic information. + +Functions +--------- +* **decon**: This is a wrapper function for all other microDecon functions. t first decontaminates the data using remove.cont(), then it runs remove.thresh(), then it runs decon.diff(). +* **remove.cont**: This is the primary function for removing contamination. It outputs a single OTU table of decontaminated results (OTUs that were entirely contamination are still included as rows of 0s). +* **remove.thresh**: This function removes residual contamination in the output from remove.cont(). +* **decon.diff**: This function takes the output of either remove.cont() or remove.thresh() as well your original, contaminated data, and it returns summary statistics of how many OTUs were removed. + +Outputs +-------- +* **Decontaminated table**: A table of decontaminated OTU data. +* **Reads removed**: An OTU table showing the number of removed reads form each OTU. +* **Difference sum**: The total number of removed reads from each OTU that amplified in the blank. +* **Difference mean**: The average number of removed reads from each OTU that amplified in the blank. +* **removed OTUs**: A table including the OTU identifiers which were completely removed from either particular groups or the entire data set. + +For further information visit the complete `docs <https://github.com/donaldtmcknight/microDecon/blob/master/microDecon%20user's%20guide%201.0.2%20updated.pdf>`_ + +]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file